A study was to investigate the regulation of bone marrow mesenchymal stem cells (BMSCs) on the stemness of hypopharyngeal cancer cells (FaDu cells). Green fluorescent protein-labeled FaDu cells were cocultured with BMSCs and then were isolated. In vitro experiments, including cell cycle and apoptosis analyses and clonogenic and sphere formation assays, were conducted using the cocultured FaDu cells to determine the stemness of FaDu cells. The tumor formation assay was performed through subcutaneous injection of FaDu cells into nude mice to determine the tumorigenic ability of FaDu cells after coculture. Immunohistochemical analysis of CD44 and ALDH1 was performed on the tumor tissue. After coculturing with human BMSCs, the ratio of FaDu cells at G2 phase was increased, while the ratios at S and G1 phases were decreased. In addition, coculture reduced apoptosis, but increased the clonogenic ability and sphere formation efficiency of FaDu cells. Finally, coculturing FaDu cells induced more robust and faster tumor formation as well as increased expression levels of CD44 and ALDH1 in tumor tissue. BMSCs promote the stemness of hypopharyngeal cancer cells.